working commit of the fmx-assign-to-gt functionality

[erflynn]

Addresses #23

Adds optional function to run gtcheck to compare reference vcf and freemuxlet output.

[erflynn]

@amadeovezz -- can you check that these additions to the pre_qc file follow conventions you have set up for channels? would love feedback on this.

[amadeovezz]

As intuitive as it may be to add this logic under the freemuxlet conditionals, I think conceptually and for readability it is better to put this after the de-multiplexing stage. That way we can leave the intention of block entirely for de-multiplexing and the outputs of de-multiplexing flow into the FMX_ASSIGN_TO_GT process. How do you feel about adding it on line 263 (after de-multiplexing). Something like:

if (params.settings.demux_method == "freemuxlet" && params.settings.fmx_assign_to_gt) {
    if (params.settings.merge) {
        FMX_ASSIGN_TO_GT(
            Channel.from(get_pool_vcf())
                .join(FREEMUXLET_POOL.out.vcf) // [pool, ref_vcf, fmx_vcf]
        );
    }

    ch_gt_input = Channel.from(get_pool_vcf()) // [pool, vcf]
        .combine(
            Channel.from(get_library_by_pool()).map { it -> [it[1], it[0]] }, 
            by: 0
        ) // [pool, vcf, lib]
        .map { it -> [it[2], it[1]] } // [lib, vcf]
        .join(FREEMUXLET_LIBRARY.out.vcf); // [lib, ref_vcf, fmx_vcf]

    // TODO: add checks that the reference file exists
    FMX_ASSIGN_TO_GT_LIBRARY(ch_gt_input);
}

This also de-duplicates some of the repeated code for the single library processing

[erflynn]

Ooo good call. I'll move it around, thanks!

[amadeovezz]

I'm happy you unified these processes!

I remember now why I duplicated it as a short term solution. There are other pipelines that reference SEPARATE_FMX and I wanted to make sure I didnt break them by being explicit about the input:

tuple val(library), path(vcf_file), path(sample_file), path(lmix_file)

Might be worth running those pipelines to be sure?

[amadeovezz]

@erflynn granted my hotfix testing PR works (and the subsequently merged in). Do you want to try and adding a test cases for this? Seems like a good candidate.

[amadeovezz]

so I think you can take this line and lines 180-186 and move them to the conditional below.

[amadeovezz]

the channels FREEMUXLET_LIBRARY.out.vcf and SEPARATE_FMX will continue to exist. And that way we encapsulate everything into the conditional

[erflynn]

thanks! just updated

[amadeovezz]

@amadeovezz -- can you check that these additions to the pre_qc file follow conventions you have set up for channels? would love feedback on this.

ya i was actually looking at the channel logic, i think we can refactor it to make it simpler.